[med-svn] [Git][med-team/python-datacache][upstream] New upstream version 1.4.1

Alexandre Detiste (@detiste-guest) gitlab at salsa.debian.org
Sun Sep 22 12:44:03 BST 2024



Alexandre Detiste pushed to branch upstream at Debian Med / python-datacache


Commits:
1b2c5769 by Alexandre Detiste at 2024-09-22T13:37:10+02:00
New upstream version 1.4.1
- - - - -


16 changed files:

- PKG-INFO
- README.md
- datacache.egg-info/PKG-INFO
- datacache.egg-info/SOURCES.txt
- datacache/__init__.py
- datacache/common.py
- datacache/database_types.py
- datacache/download.py
- datacache/version.py
- test/test_cache_object.py → tests/test_cache_object.py
- test/test_database_objects.py → tests/test_database_objects.py
- test/test_database_types.py → tests/test_database_types.py
- test/test_db_from_dataframes.py → tests/test_db_from_dataframes.py
- test/test_download.py → tests/test_download.py
- test/test_fasta_dict.py → tests/test_fasta_dict.py
- test/test_names.py → tests/test_names.py


Changes:

=====================================
PKG-INFO
=====================================
@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: datacache
-Version: 1.2.1
+Version: 1.4.1
 Summary: Helpers for transparently downloading datasets
 Home-page: https://github.com/openvax/datacache
 Author: Alex Rubinsteyn
@@ -15,29 +15,32 @@ Classifier: Programming Language :: Python
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: pandas>=0.15.2
+Requires-Dist: appdirs>=1.4.0
+Requires-Dist: progressbar33>=2.4
+Requires-Dist: requests>=2.5.1
+Requires-Dist: typechecks>=0.0.2
+Requires-Dist: mock
 
-<a href="https://travis-ci.org/openvax/datacache">
-    <img src="https://travis-ci.org/openvax/datacache.svg?branch=master" alt="Build Status" />
-</a>
+[![Tests](https://github.com/openvax/datacache/actions/workflows/tests.yml/badge.svg)](https://github.com/openvax/datacache/actions/workflows/tests.yml)
 <a href="https://coveralls.io/github/openvax/datacache?branch=master">
-    <img src="https://coveralls.io/repos/openvax/datacache/badge.svg?branch=master&service=github" alt="Coverage Status" />
+<img src="https://coveralls.io/repos/openvax/datacache/badge.svg?branch=master&service=github" alt="Coverage Status" />
 </a>
 <a href="https://pypi.python.org/pypi/datacache/">
-    <img src="https://img.shields.io/pypi/v/datacache.svg?maxAge=1000" alt="PyPI" />
+<img src="https://img.shields.io/pypi/v/datacache.svg?maxAge=1000" alt="PyPI" />
 </a>
 
-DataCache
-=========
+# DataCache
 
 Helpers for transparently downloading datasets
 
 ## API
 
-* **fetch_file**(download_url, filename = *None*, decompress = *False*, subdir = *None*)
-* **fetch_and_transform**(transformed_filename, transformer, loader,
-        source_filename, source_url, subdir = *None*)
-* **fetch_fasta_dict**(download_url, filename = *None*, subdir = *None*)
-* **fetch_fasta_db**(table_name, download_url, fasta_filename = *None*,
-        key_column = *'id'*, value_column = *'seq'*, subdir = *None*)
-* **fetch_csv_db**(table_name, download_url, csv_filename = *None*, subdir = *None*,
-        \*\*pandas_kwargs)
+- **fetch_file**(download*url, filename = \_None*, decompress = _False_, subdir = _None_)
+- **fetch_and_transform**(transformed*filename, transformer, loader,
+  source_filename, source_url, subdir = \_None*)
+- **fetch_fasta_dict**(download*url, filename = \_None*, subdir = _None_)
+- **fetch_fasta_db**(table*name, download_url, fasta_filename = \_None*,
+  key*column = *'id'_, value_column = _'seq'_, subdir = \_None_)
+- **fetch_csv_db**(table*name, download_url, csv_filename = \_None*, subdir = _None_,
+  \*\*pandas_kwargs)


=====================================
README.md
=====================================
@@ -1,25 +1,22 @@
-<a href="https://travis-ci.org/openvax/datacache">
-    <img src="https://travis-ci.org/openvax/datacache.svg?branch=master" alt="Build Status" />
-</a>
+[![Tests](https://github.com/openvax/datacache/actions/workflows/tests.yml/badge.svg)](https://github.com/openvax/datacache/actions/workflows/tests.yml)
 <a href="https://coveralls.io/github/openvax/datacache?branch=master">
-    <img src="https://coveralls.io/repos/openvax/datacache/badge.svg?branch=master&service=github" alt="Coverage Status" />
+<img src="https://coveralls.io/repos/openvax/datacache/badge.svg?branch=master&service=github" alt="Coverage Status" />
 </a>
 <a href="https://pypi.python.org/pypi/datacache/">
-    <img src="https://img.shields.io/pypi/v/datacache.svg?maxAge=1000" alt="PyPI" />
+<img src="https://img.shields.io/pypi/v/datacache.svg?maxAge=1000" alt="PyPI" />
 </a>
 
-DataCache
-=========
+# DataCache
 
 Helpers for transparently downloading datasets
 
 ## API
 
-* **fetch_file**(download_url, filename = *None*, decompress = *False*, subdir = *None*)
-* **fetch_and_transform**(transformed_filename, transformer, loader,
-        source_filename, source_url, subdir = *None*)
-* **fetch_fasta_dict**(download_url, filename = *None*, subdir = *None*)
-* **fetch_fasta_db**(table_name, download_url, fasta_filename = *None*,
-        key_column = *'id'*, value_column = *'seq'*, subdir = *None*)
-* **fetch_csv_db**(table_name, download_url, csv_filename = *None*, subdir = *None*,
-        \*\*pandas_kwargs)
+- **fetch_file**(download*url, filename = \_None*, decompress = _False_, subdir = _None_)
+- **fetch_and_transform**(transformed*filename, transformer, loader,
+  source_filename, source_url, subdir = \_None*)
+- **fetch_fasta_dict**(download*url, filename = \_None*, subdir = _None_)
+- **fetch_fasta_db**(table*name, download_url, fasta_filename = \_None*,
+  key*column = *'id'_, value_column = _'seq'_, subdir = \_None_)
+- **fetch_csv_db**(table*name, download_url, csv_filename = \_None*, subdir = _None_,
+  \*\*pandas_kwargs)


=====================================
datacache.egg-info/PKG-INFO
=====================================
@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: datacache
-Version: 1.2.1
+Version: 1.4.1
 Summary: Helpers for transparently downloading datasets
 Home-page: https://github.com/openvax/datacache
 Author: Alex Rubinsteyn
@@ -15,29 +15,32 @@ Classifier: Programming Language :: Python
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: pandas>=0.15.2
+Requires-Dist: appdirs>=1.4.0
+Requires-Dist: progressbar33>=2.4
+Requires-Dist: requests>=2.5.1
+Requires-Dist: typechecks>=0.0.2
+Requires-Dist: mock
 
-<a href="https://travis-ci.org/openvax/datacache">
-    <img src="https://travis-ci.org/openvax/datacache.svg?branch=master" alt="Build Status" />
-</a>
+[![Tests](https://github.com/openvax/datacache/actions/workflows/tests.yml/badge.svg)](https://github.com/openvax/datacache/actions/workflows/tests.yml)
 <a href="https://coveralls.io/github/openvax/datacache?branch=master">
-    <img src="https://coveralls.io/repos/openvax/datacache/badge.svg?branch=master&service=github" alt="Coverage Status" />
+<img src="https://coveralls.io/repos/openvax/datacache/badge.svg?branch=master&service=github" alt="Coverage Status" />
 </a>
 <a href="https://pypi.python.org/pypi/datacache/">
-    <img src="https://img.shields.io/pypi/v/datacache.svg?maxAge=1000" alt="PyPI" />
+<img src="https://img.shields.io/pypi/v/datacache.svg?maxAge=1000" alt="PyPI" />
 </a>
 
-DataCache
-=========
+# DataCache
 
 Helpers for transparently downloading datasets
 
 ## API
 
-* **fetch_file**(download_url, filename = *None*, decompress = *False*, subdir = *None*)
-* **fetch_and_transform**(transformed_filename, transformer, loader,
-        source_filename, source_url, subdir = *None*)
-* **fetch_fasta_dict**(download_url, filename = *None*, subdir = *None*)
-* **fetch_fasta_db**(table_name, download_url, fasta_filename = *None*,
-        key_column = *'id'*, value_column = *'seq'*, subdir = *None*)
-* **fetch_csv_db**(table_name, download_url, csv_filename = *None*, subdir = *None*,
-        \*\*pandas_kwargs)
+- **fetch_file**(download*url, filename = \_None*, decompress = _False_, subdir = _None_)
+- **fetch_and_transform**(transformed*filename, transformer, loader,
+  source_filename, source_url, subdir = \_None*)
+- **fetch_fasta_dict**(download*url, filename = \_None*, subdir = _None_)
+- **fetch_fasta_db**(table*name, download_url, fasta_filename = \_None*,
+  key*column = *'id'_, value_column = _'seq'_, subdir = \_None_)
+- **fetch_csv_db**(table*name, download_url, csv_filename = \_None*, subdir = _None_,
+  \*\*pandas_kwargs)


=====================================
datacache.egg-info/SOURCES.txt
=====================================
@@ -15,10 +15,10 @@ datacache.egg-info/SOURCES.txt
 datacache.egg-info/dependency_links.txt
 datacache.egg-info/requires.txt
 datacache.egg-info/top_level.txt
-test/test_cache_object.py
-test/test_database_objects.py
-test/test_database_types.py
-test/test_db_from_dataframes.py
-test/test_download.py
-test/test_fasta_dict.py
-test/test_names.py
\ No newline at end of file
+tests/test_cache_object.py
+tests/test_database_objects.py
+tests/test_database_types.py
+tests/test_db_from_dataframes.py
+tests/test_download.py
+tests/test_fasta_dict.py
+tests/test_names.py
\ No newline at end of file


=====================================
datacache/__init__.py
=====================================
@@ -29,6 +29,7 @@ from .cache import Cache
 from .version import __version__
 
 __all__ = [
+    '__version__',
     'fetch_file',
     'fetch_and_transform',
     'fetch_csv_dataframe',


=====================================
datacache/common.py
=====================================
@@ -45,7 +45,7 @@ def normalize_filename(filename):
     Remove special characters and shorten if name is too long
     """
     # if the url pointed to a directory then just replace all the special chars
-    filename = re.sub("/|\\|;|:|\?|=", "_", filename)
+    filename = re.sub(r"/|\\|;|:|\?|=", "_", filename)
 
     if len(filename) > 150:
         prefix = hashlib.md5(filename).hexdigest()


=====================================
datacache/database_types.py
=====================================
@@ -38,6 +38,7 @@ _dtype_to_db_type_dict = {
     'object_': 'TEXT',
     'string_': 'TEXT',
     'str': 'TEXT',
+    'category': 'TEXT',
 }
 
 def _lookup_type_name(type_name):


=====================================
datacache/download.py
=====================================
@@ -13,6 +13,7 @@
 import gzip
 import logging
 import os
+import errno
 import subprocess
 from shutil import move
 from tempfile import NamedTemporaryFile
@@ -78,7 +79,7 @@ def _download_to_temp_file(
             logger.info("Running: %s" % (" ".join(wget_command_list)))
             subprocess.call(wget_command_list)
         except OSError as e:
-            if e.errno == os.errno.ENOENT:
+            if e.errno == errno.ENOENT:
                 # wget not found
                 download_using_python()
             else:


=====================================
datacache/version.py
=====================================
@@ -1,3 +1,3 @@
-__version__ = '1.2.1'
+__version__ = '1.4.1'
 
 


=====================================
test/test_cache_object.py → tests/test_cache_object.py
=====================================


=====================================
test/test_database_objects.py → tests/test_database_objects.py
=====================================


=====================================
test/test_database_types.py → tests/test_database_types.py
=====================================


=====================================
test/test_db_from_dataframes.py → tests/test_db_from_dataframes.py
=====================================


=====================================
test/test_download.py → tests/test_download.py
=====================================


=====================================
test/test_fasta_dict.py → tests/test_fasta_dict.py
=====================================


=====================================
test/test_names.py → tests/test_names.py
=====================================



View it on GitLab: https://salsa.debian.org/med-team/python-datacache/-/commit/1b2c5769be76136661a15b1ed8cf6759ceaa448d

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-datacache/-/commit/1b2c5769be76136661a15b1ed8cf6759ceaa448d
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